Yes- like all good decaf beans, its swiss water process which removes the majority of the caffeine. Swiss Water claim 99.9% caffeine free. See http://www.swisswater.com/
Id be very surprised if any cafe would substitute caffeinated coffee for decaf. Other than the fact you didnt sleep, what evidence do you have?* :-?
My personal opinion is that one caffeinated coffee per day is fine. If your partner is accustomed to caffeine, its possibly more harmful to simply cease.